CELL BIOLOGY-PROTEINS

1. CELL BIOLOGY - BIOMOLECULES INTRODUCTION

2. CARBOHYDRATES

3. PROTEINS

4. LIPIDS

5. NUCLEIC ACIDS

6. ENZYMES

1. Proteins

•The term 'protein' was first coined by Berzelius (1837) and Mulder (1838).

•These are involved in the functions like structural support, transport, storage, signalling etc.

•Protein is a Greek word meaning "Primary" or "in the lead".

•Proteins can be defined as polymer of amino-acids (Fisher and Hofmeister).

• There are approximately 300 amino acids known to exist out of which only 20 are used in the formation of proteins.

• Proteins are most diverse molecules in a cell.

•The general structure of proteins is given below:



General Structure of Protein.

2. Amino Acids

• Amino acids are small molecules composed of carbon, hydrogen, oxygen , nitrogen and in few cases sulphur also.

• Generally, only 20 types of amino acids are used in the formation of proteins.

•Amino-acids are amphoteric in nature due to the presence of both -COOH (acidic group) and -NH2 (basic group).

a. Structure of Amino - Acids

Structure of Amino Acid.

Classification of amino acids on the basis of synthesis in body of organism :

Essential Amino Acids Non-Essential Amino Acids Semi Essential Amino Acids
These are not synthesised in the body of organism and are to be obtained from diet. These are synthesised in the body of organism and not necessarily to be obtained via diet. These amino acids are synthesized in very less amount in animal cells. Thus, their presence is important in food.'
Examples: Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine. Examples: Alanine, Asparagine, Aspartic acid, and Glutamic acid. Examples: Histidine, Arginine


Figure showing different amino acids on the basis of side chain and chemical nature.

b. Zwitter Ion

•Amino acids possess ionisable groups as -NH2 and -COOH.

•Due to these groups amino acids have different structure in solutions at different pH.

•Amino acid acts as Dipolar ion (amino acids possess both positive and negative charge hence called Zwitter ion).

•The pH at which amino acid acts as a Zwitter ion is known as isoelectric pH.

Neutral pH Acidic Solution Basic Solution

Amino Acid acts as Dipolar..

It has the ability to accept or donate H+ ions.

Amino acid is Positively charged.

It has the ability to accept H+ ions

Amino acid is Negatively charged.

It has the ability to donate H+ ions.



Structures of Amino Acid at different pH.

c. Classification of Amino Acids

i.Neutral Amino Acids:

•They have equal number of amino (NH2) and carboxylic acid (COOH)groups.

ii.Acidic Amino Acids:

•The amino acids contain carboxylic acid (COOH)group on their side chains at neutral pH.

iii. Basic Amino ACids:

•The amino acids contain amino (NH2)group on their side chains at neutral pH.

•Based on the presence of NH2 and COO- groups the amino acids are classified as given below:

Classification of Amino Acids.

d. Peptide Bond

•It is also known as amide bond.

•It is formed between the amino group of one amino acid and carboxyl group of another amino acid.

•This is a dehydration reaction (loss of H2O)also known as condensation reaction.

•It is a planar.

•Sequence of amino acids with less than 50 amino acids is known as peptide while as the term protein or polypeptide is used for longer sequences

Peptide Bond Formation.



• Based on the increasing complexity in structure proteins are classified as below:

(a) Simple Proteins:

•These are composed of only one amino acid.

•Simple proteins are further classified into two types:



(i) Globular Proteins:

•These have an axial ratio (length: width) of less than 10 (usually not over 3 or 4) and, henceforth, possess a relatively spherical or ovoid shape.

•As a class, globular proteins are more complex in conformation than fibrous proteins, perform variable biological functions and are dynamic in their activities.

•Tertiary and quaternary structures are usually linked with this class of proteins.

•Generally all enzymes are globular proteins, as are protein hormones, blood transport proteins, antibodies and nutrient storage proteins.

→Example: egg albumin, serum, globulins.



(ii) Fibrous Protein:

•These have axial ratios greater than 10 and, henceforth, resemble long ribbons or fibres in shape.

•These are mainly of animal origin.

•Fibrous proteins are insoluble in all common solvents such as water.

•Most fibrous proteins are found in a structural or protective role.

→Example: hairs, claws



(b) Conjugated Proteins:

•These are also of globular type except for the pigment in chicken feathers which is probably of fibrous nature.

• Separable nonprotein portion linked with these proteins is termed as prosthetic group.

• The prosthetic group can be a metal or a compound.

•The various divisions included in this class are Nucleoproteins, Mucoproteins, Glycoproteins, Chromoproteins, Metalloproteins, Lipoproteins, Phosphoproteins.



(c) Derived Proteins:

•These are derivatives of proteins resulting from the action of heat, enzymes or chemical reagents.

•This group also includes the artificially-produced polypeptides.



(i) Primary Derived Proteins.

• These are derivatives of proteins in which the size of protein molecule is not altered materially.

→ Example: Fibrin, Myosin



(ii) Secondary Derived Proteins.

• These are derivatives of proteins in which the hydrolysis has certainly occurred.

•The molecules are, as a rule, smaller than the original proteins.

→ Example: Peptones, Peptides.



3. Structural Stages of Protein

(a) Primary Structure:

•It can be defined as the simplest form of configuration involving linear alignment of amino acids linked by peptide bonds.

• The primary structure of the protein begins from amino terminal end and ends at carboxy terminal end.

•The end of the peptide with free carboxylic group is known as carboxy terminal while as the end with a free amino group is known as amino terminal.

•The amino acid sequence makes up the primary structure of the protein.

•The chemical and biological properties of the protein totally dependent upon the secondary and tertiary structure of proteins.



(b) Secondary Structure:

•Local structural conformations depending upon hydrogen bonding lead to secondary structure of proteins.

•The two main types of secondary structure are: the α - helix and the β - sheet.



i.α - helix:

•The α - helix is a right-handed coiled strand. In an α-helix the side-chain substituents of the amino acid groups extend to the outside.

•Hydrogen bonds form between the oxygen of the C=O of each peptide bond in the strand and the hydrogen of the N-H group of the peptide bond, four amino acids below it in the helix.

•The hydrogen bonds make this structure especially stable.

•The side-chain substituents of the amino acids fit in beside the N-H groups.

→Example: Keratin, Myosin.



ii.β - sheet:

•The hydrogen bonding in a β - sheet is inter-strands rather than intra-strands.

•The sheet conformation consists of pairs of strands lying side-by-side.

•The carbonyl oxygens in one strand hydrogen bond with the amino hydrogens of the adjacent strand.

• The two strands can be parallel or anti-parallel depending on whether the strand directions (N-terminus to C-terminus) are the same or opposite.

•Due to more well-aligned hydrogen bonds the anti-parallel β - sheet is more stable.

→Example: Fibroin (Silk)



(c) Tertiary Structure:

•Tertiary structure can be defined as the overall three-dimensional shape of an entire protein molecule.

•In order to achieve maximum stability the protein molecule will bend and twist in such a way as to achieve maximum stability or lowest energy state.

• Although the three-dimensional shape of a protein may seem irregular and random, it involves many stabilizing forces due to bonding interactions between the side-chain groups of the amino acids.

•Interactions involve mainly hydrophobic interactions.

•Additionally, hydrogen bonds may form between different side-chain groups.

•Other interactions involved in stabilizing tertiary structure are Salt bridges, ionic interactions between positively and negatively charged sites on amino acid side chains. Majority of the proteins in the protoplasm exhibit tertiary structure.



(d) Quaternary Structure:

•Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits.

•These subunits may be the same termed as in a homodimer or different called as in a heterodimer conformation.

•The quaternary structure refers to how these protein subunits interact with each other and arrange themselves to form a larger aggregate protein complex.

•The final shape of the protein complex is once again stabilized by various interactions, that includes hydrogen-bonds, disulphide-bridges and salt bridges.

•Adult human haemoglobin exhibits quaternary structure.

Diagrammatic representation of structural stages of proteins: